LAMMPS (12 Jun 2025 - Development - patch_12Jun2025-739-g2644e7f6fa-modified)
  using 1 OpenMP thread(s) per MPI task
# Solvated 5-mer peptide, run for 8ps in NVT

units           real
atom_style      full

pair_style      lj/charmm/coul/long 8.0 10.0 10.0
bond_style      harmonic
angle_style     charmm
dihedral_style  charmm
improper_style  harmonic
kspace_style    pppm 0.0001

read_data       data.peptide
Reading data file ...
  orthogonal box = (36.840194 41.013691 29.768095) to (64.21156 68.385058 57.139462)
  1 by 2 by 2 MPI processor grid
  reading atoms ...
  2004 atoms
  reading velocities ...
  2004 velocities
  scanning bonds ...
  3 = max bonds/atom
  scanning angles ...
  6 = max angles/atom
  scanning dihedrals ...
  14 = max dihedrals/atom
  scanning impropers ...
  1 = max impropers/atom
  orthogonal box = (36.840194 41.013691 29.768095) to (64.21156 68.385058 57.139462)
  1 by 2 by 2 MPI processor grid
  reading bonds ...
  1365 bonds
  reading angles ...
  786 angles
  reading dihedrals ...
  207 dihedrals
  reading impropers ...
  12 impropers
Finding 1-2 1-3 1-4 neighbors ...
  special bond factors lj:    0        0        0       
  special bond factors coul:  0        0        0       
     4 = max # of 1-2 neighbors
     7 = max # of 1-3 neighbors
    14 = max # of 1-4 neighbors
    18 = max # of special neighbors
  special bonds CPU = 0.000 seconds
  read_data CPU = 0.014 seconds

neighbor        2.0 bin
neigh_modify    delay 5

thermo          50
#dump            dump1 all atom 100 peptide.dump

timestep        8

run_style respa 3 2 8 bond 1 dihedral 2 pair 2 kspace 3
Respa levels:
  1 = bond angle
  2 = dihedral improper pair
  3 = kspace

fix             1 all nvt temp 250.0 250.0 100.0 tchain 1
fix             cor all filter/corotate m 1.0
  19 = # of size 2 clusters
  0 = # of size 3 clusters
  3 = # of size 4 clusters
  0 = # of size 5 clusters
  646 = # of frozen angles
run             1000

CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE

Your simulation uses code contributions which should be cited:

- Mollified Impulse Method with Corotational Filter: doi:10.1016/j.jcp.2016.12.024

@Article{Fath2017,
 Title ={A Fast Mollified Impulse Method for Biomolecular Atomistic Simulations},
 Author = {L. Fath and M. Hochbruck and C. V. Singh},
 Journal = {Journal of Computational Physics},
 Year = {2017},
 Pages = {180--198},
 Volume = {333},

 Doi = {https://doi.org/10.1016/j.jcp.2016.12.024},
 ISSN = {0021-9991},
 Keywords = {Mollified impulse method},
 Url = {https://www.sciencedirect.com/science/article/pii/S0021999116306787}
}

CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE

PPPM initialization ...
  using 12-bit tables for long-range coulomb
  G vector (1/distance) = 0.26872465
  grid = 15 15 15
  stencil order = 5
  estimated absolute RMS force accuracy = 0.022820853
  estimated relative force accuracy = 6.872432e-05
  using double precision FFTW3
  3d grid and FFT values/proc = 4312 960
Generated 91 of 91 mixed pair_coeff terms from arithmetic mixing rule
Neighbor list info ...
  update: every = 1 steps, delay = 5 steps, check = yes
  max neighbors/atom: 2000, page size: 100000
  master list distance cutoff = 12
  ghost atom cutoff = 12
  binsize = 6, bins = 5 5 5
  1 neighbor lists, perpetual/occasional/extra = 1 0 0
  (1) pair lj/charmm/coul/long, perpetual
      attributes: half, newton on
      pair build: half/bin/newton
      stencil: half/bin/3d
      bin: standard
Per MPI rank memory allocation (min/avg/max) = 17.23 | 17.41 | 17.61 Mbytes
   Step          Temp          E_pair         E_mol          TotEng         Press     
         0   190.0857      -6442.7438      70.391457     -5237.4338      20361.984    
        50   239.47653     -7205.1003      1092.7665     -4682.5242     -23733.122    
       100   244.0633      -6784.9831      422.89084     -4904.8971      16449.308    
       150   241.01894     -7261.7571      959.64066     -4863.0978     -13738.272    
       200   252.32969     -6954.7014      626.43343     -4821.7177      9244.8101    
       250   246.22994     -7247.028       872.81856     -4904.0782     -8941.3148    
       300   242.36765     -6993.6899      674.75008     -4871.8686      6115.0664    
       350   252.57261     -7249.1951      799.34374     -4941.8508     -5577.4894    
       400   263.24155     -7109.2936      678.05188     -4859.5416      3513.6665    
       450   248.8095      -7266.1343      828.78223     -4951.8194     -3089.7304    
       500   256.08881     -7188.7117      745.5002      -4914.2172      2696.5037    
       550   248.39825     -7302.0046      811.47332     -5007.454      -2088.2536    
       600   250.81324     -7208.3811      818.92446     -4891.9605     -72.221002    
       650   256.4929      -7257.2571      807.44386     -4918.4063     -966.47864    
       700   249.188       -7311.3341      817.71214     -5005.8294      235.03461    
       750   245.32513     -7293.6707      857.82183     -4971.1199     -1466.0814    
       800   258.57705     -7313.1066      842.19664     -4927.0595     -1233.2518    
       850   242.28318     -7333.5962      818.9232      -5068.1061     -1159.3422    
       900   253.42808     -7315.3233      829.91793     -4972.2972     -134.02763    
       950   249.11945     -7304.1512      885.69221     -4931.0757     -1591.0534    
      1000   243.81012     -7412.5091      861.56763     -5095.258      -1380.436     
Loop time of 17.8257 on 4 procs for 1000 steps with 2004 atoms

Performance: 38.775 ns/day, 0.619 hours/ns, 56.099 timesteps/s, 112.422 katom-step/s
99.2% CPU use with 4 MPI tasks x 1 OpenMP threads

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 14.995     | 15.206     | 15.488     |   4.7 | 85.30
Bond    | 0.12397    | 0.15221    | 0.18541    |   6.6 |  0.85
Kspace  | 0.16387    | 0.16657    | 0.16824    |   0.4 |  0.93
Neigh   | 0.57651    | 0.57672    | 0.57696    |   0.0 |  3.24
Comm    | 1.1511     | 1.4118     | 1.5895     |  14.5 |  7.92
Output  | 0.00032291 | 0.00036201 | 0.0004728  |   0.0 |  0.00
Modify  | 0.25077    | 0.25249    | 0.25548    |   0.4 |  1.42
Other   |            | 0.05943    |            |       |  0.33

Nlocal:            501 ave         518 max         491 min
Histogram: 1 0 2 0 0 0 0 0 0 1
Nghost:        6673.75 ave        6716 max        6619 min
Histogram: 1 0 0 1 0 0 0 0 1 1
Neighs:         176918 ave      183982 max      171274 min
Histogram: 1 0 0 2 0 0 0 0 0 1

Total # of neighbors = 707674
Ave neighs/atom = 353.13074
Ave special neighs/atom = 2.3403194
Neighbor list builds = 200
Dangerous builds = 200
unfix           cor
unfix           1



Total wall time: 0:00:17
